RNA-seq analysis raw data format

neetu · 10-12-2011, 09:00 PM

Hello,

I am relatively new to this sequencing field. can anybody guide me with the basics and tell me what is the RNA-seq analysis raw data format. Is it .bed files or fastq files. How to find out what all files in GEO or array express is having RNA-seq data?

NicoBxl · 10-12-2011, 11:20 PM

in general it's fastq format

kopi-o · 10-13-2011, 12:37 AM

For GEO, you can find RNA-seq experiments by filtering on "series type":

http://www.ncbi.nlm.nih.gov/geo/brow...ate&display=20

On ArrayExpress, go to

http://www.ebi.ac.uk/arrayexpress/browse.html

and select "RNA assay" and "high-throughput sequencing" from two of the menus.

neetu · 10-13-2011, 12:44 AM

Thanks a lot for your reply..i will try searching..

neetu · 10-13-2011, 02:19 AM

i am actually having a problem, i opened this page from GEO
http://www.ncbi.nlm.nih.gov/projects...i?acc=GSE20116
this is an RNA-seq analysis for sure, if i need the data and i scroll down to the files attached to this page, i get .txt files and also files which say are for SRA study. now how should i take the data from this page? can the data be in .txt format also. also want to know where can we use the data from SRA study.

ulz_peter · 10-13-2011, 02:34 AM

For introduction to RNA-seq see: http://seqanswers.com/wiki/How-to/RNASeq_analysis

and: sometimes fastq files got the ending .txt as windows users won't recognize text files as such if they do not have this ending. They may be fastq files even with the .txt ending. (I haven't looked into these files, they may be something else as well)

dpryan · 10-13-2011, 04:22 AM

If you click on one of the samples (e.g. going to here) and look in the "Data processing" section, they mention the file type and where to find the actual specification for it. The SRA files could be converted to fastq format with the SRA toolkit. I should note, whether you actually want to redo the alignment yourself (i.e. downloading the SRA files, converting them to fastq, alignment with tophat or whatever) or directly use the prealigned files depends a bit on what your goals are.

BTW, if you need the reads aligned to hg19 instead of hg18, you can google for the very useful "liftOver" tool.

neetu · 10-14-2011, 02:15 AM

thanks a ton for your reply dpryan and peter. your links are really helpful. one more doubt now arises is that is there a way by which we can get prealigned files. i till now presumed that we get only RAW data from GEO and AE, and we have to compulsorily align it to process further. Can we get SAM and BAM files also ?

dpryan · 10-14-2011, 02:23 AM

Unfortunately I don't think there's a single answer to that question that applies to all datasets. I've used a number of datasets that provided prealigned BED or similar files, but that's certainly not the case with all of them.

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10-12-2011, 09:00 PM	#1
neetu Member Location: India Join Date: Oct 2011 Posts: 11	RNA-seq analysis raw data format Hello, I am relatively new to this sequencing field. can anybody guide me with the basics and tell me what is the RNA-seq analysis raw data format. Is it .bed files or fastq files. How to find out what all files in GEO or array express is having RNA-seq data?

10-12-2011, 11:20 PM	#2
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	in general it's fastq format

10-13-2011, 12:37 AM	#3
kopi-o Senior Member Location: Stockholm, Sweden Join Date: Feb 2008 Posts: 319	For GEO, you can find RNA-seq experiments by filtering on "series type": http://www.ncbi.nlm.nih.gov/geo/brow...ate&display=20 On ArrayExpress, go to http://www.ebi.ac.uk/arrayexpress/browse.html and select "RNA assay" and "high-throughput sequencing" from two of the menus.

10-13-2011, 12:44 AM	#4
neetu Member Location: India Join Date: Oct 2011 Posts: 11	Thanks a lot for your reply..i will try searching..

10-13-2011, 02:19 AM	#5
neetu Member Location: India Join Date: Oct 2011 Posts: 11	i am actually having a problem, i opened this page from GEO http://www.ncbi.nlm.nih.gov/projects...i?acc=GSE20116 this is an RNA-seq analysis for sure, if i need the data and i scroll down to the files attached to this page, i get .txt files and also files which say are for SRA study. now how should i take the data from this page? can the data be in .txt format also. also want to know where can we use the data from SRA study.

10-13-2011, 02:34 AM	#6
ulz_peter Senior Member Location: Graz, Austria Join Date: Feb 2010 Posts: 219	For introduction to RNA-seq see: http://seqanswers.com/wiki/How-to/RNASeq_analysis and: sometimes fastq files got the ending .txt as windows users won't recognize text files as such if they do not have this ending. They may be fastq files even with the .txt ending. (I haven't looked into these files, they may be something else as well)

10-13-2011, 04:22 AM	#7
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	If you click on one of the samples (e.g. going to here) and look in the "Data processing" section, they mention the file type and where to find the actual specification for it. The SRA files could be converted to fastq format with the SRA toolkit. I should note, whether you actually want to redo the alignment yourself (i.e. downloading the SRA files, converting them to fastq, alignment with tophat or whatever) or directly use the prealigned files depends a bit on what your goals are. BTW, if you need the reads aligned to hg19 instead of hg18, you can google for the very useful "liftOver" tool.

10-14-2011, 02:15 AM	#8
neetu Member Location: India Join Date: Oct 2011 Posts: 11	thanks a ton for your reply dpryan and peter. your links are really helpful. one more doubt now arises is that is there a way by which we can get prealigned files. i till now presumed that we get only RAW data from GEO and AE, and we have to compulsorily align it to process further. Can we get SAM and BAM files also ?

10-14-2011, 02:23 AM	#9
dpryan Devon Ryan Location: Freiburg, Germany Join Date: Jul 2011 Posts: 3,480	Unfortunately I don't think there's a single answer to that question that applies to all datasets. I've used a number of datasets that provided prealigned BED or similar files, but that's certainly not the case with all of them.